PR#3: Fix member read size mistake, especially on big endian (#1930943) - rpms/inchi

rpms / inchi

#3 Fix member read size mistake, especially on big endian (#1930943)

Closed 2 years ago by rathann. Opened 2 years ago by mtasaka.

rpms/ mtasaka/inchi s390x-fix into rawhide

Fix member read size mistake, especially on big endian (#1930943)

Mamoru TASAKA • 2 years ago

6ef0b9e

inchi-1.0.6-0001-MolfileReadCountsLine-fix-storing-n_atoms-n_bonds-me.patch

file added

+62

		`@@ -0,0 +1,62 @@`
		`+ From 26351733bde20eb16aedd62b4b64a2417615020e Mon Sep 17 00:00:00 2001`
		`+ From: Mamoru TASAKA <mtasaka@fedoraproject.org>`
		`+ Date: Thu, 25 Nov 2021 23:07:31 +0900`
		`+ Subject: [PATCH] MolfileReadCountsLine: fix storing n_atoms, n_bonds members`
		`+ after reading short size`
		`+`
		`+ In MolfileReadCountsLine() (in INCHI_BASE/src/mol_fmt1.c), currently`
		`+ ctab->n_atoms and ctab->n_bonds, which have int type (as defined in src/mol_fmt.h),`
		`+ are passed to be MolfileReadField(), and to be treated there as if they have`
		`+ short size (as MOL_FMT_SHORT_INT_DATA is also passed to the argument of`
		`+ MolfileReadField(), and also the comment shows).`
		`+`
		`+ This causes a error on big endian system such as s390x, where for example`
		`+ reading the line:`
		`+`
		`+ 1 0 0 0 0 0 0 0 0 0999 V2000`
		`+`
		`+ On little endian (64bit) system, ctab->n_atoms is correctly stored as 1, but on`
		`+ s390x (big endian 64bit) system, ctab->n_atoms gets 65536 (= 1<<16), which is`
		`+ unexpected.`
		`+`
		`+ To fix this, once store the read value to short size local variable, then`
		`+ copy the value to ctab->n_atoms or so later.`
		`+ ---`
		`+ INCHI_BASE/src/mol_fmt1.c \| 7 +++++--`
		`+ 1 file changed, 5 insertions(+), 2 deletions(-)`
		`+`
		`+ diff --git a/INCHI_BASE/src/mol_fmt1.c b/INCHI_BASE/src/mol_fmt1.c`
		`+ index 41ed15e..c2ad11a 100644`
		`+ --- a/INCHI_BASE/src/mol_fmt1.c`
		`+ +++ b/INCHI_BASE/src/mol_fmt1.c`
		`+ @@ -572,6 +572,7 @@ int MolfileReadCountsLine( MOL_FMT_CTAB* ctab,`
		`+ char line[MOL_FMT_INPLINELEN];`
		`+ const int line_len = sizeof( line );`
		`+ int err = 0, len;`
		`+ + short n_atoms, n_bonds;`
		`+`
		`+ p = inchi_fgetsLf( line, line_len, inp_file );`
		`+`
		`+ @@ -588,8 +589,8 @@ int MolfileReadCountsLine( MOL_FMT_CTAB* ctab,`
		`+ TREAT_ERR( err, 0, "Too long counts line" ); /* too long input file line */`
		`+ }`
		`+`
		`+ - if (0 > MolfileReadField( &ctab->n_atoms, 3, MOL_FMT_SHORT_INT_DATA, &p ) /* V2000 only: short int */`
		`+ - \|\| 0 > MolfileReadField( &ctab->n_bonds, 3, MOL_FMT_SHORT_INT_DATA, &p ) /* V2000 only: short int */`
		`+ + if (0 > MolfileReadField( &n_atoms, 3, MOL_FMT_SHORT_INT_DATA, &p ) /* V2000 only: short int */`
		`+ + \|\| 0 > MolfileReadField( &n_bonds, 3, MOL_FMT_SHORT_INT_DATA, &p ) /* V2000 only: short int */`
		`+`
		`+ #if ( MOL_FMT_QUERY == MOL_FMT_PRESENT )`
		`+ \|\| 0 > MolfileReadField( &ctab->n_atom_lists, 3, MOL_FMT_SHORT_INT_DATA, &p )`
		`+ @@ -621,6 +622,8 @@ int MolfileReadCountsLine( MOL_FMT_CTAB* ctab,`
		`+ AddErrorMessage( pStrErr, line );`
		`+ goto err_fin;`
		`+ }`
		`+ + ctab->n_atoms = n_atoms;`
		`+ + ctab->n_bonds = n_bonds;`
		`+`
		`+ /* Get CTFile version (V2000 or other) */`
		`+ len = MolfileReadField( ctab->version_string,`
		`+ --`
		`+ 2.33.1`
		`+`

inchi.spec

file modified

+8 -6

		`@@ -4,12 +4,15 @@`
		`Summary: The IUPAC International Chemical Identifier library`
		`Name: inchi`
		`Version: 1.0.6`
		`- Release: 2%{?dist}`
		`+ Release: 3%{?dist}`
		`URL: https://www.inchi-trust.org/about-the-inchi-standard/`
		`Source0: https://www.inchi-trust.org/download/%{url_ver}/INCHI-1-SRC.zip`
		`Source1: https://www.inchi-trust.org/download/%{url_ver}/INCHI-1-DOC.zip`
		`Source2: https://www.inchi-trust.org/download/%{url_ver}/INCHI-1-TEST.zip`
		`Patch0: %{name}-rpm.patch`
		`+ # reported upstream:`
		`+ # https://sourceforge.net/p/inchi/bugs/77/`
		`+ Patch1: %{name}-1.0.6-0001-MolfileReadCountsLine-fix-storing-n_atoms-n_bonds-me.patch`
		`License: LGPLv2+`
		`BuildRequires: dos2unix`
		`BuildRequires: gcc`
		`@@ -60,6 +63,7 @@`
		`%prep`
		`%setup -q -n INCHI-1-SRC -a 1 -a 2`
		`%patch0 -p1 -b .r`
		`+ %patch1 -p1 -b .big_endian`
		`for file in readme.txt ; do`
		`dos2unix -k $file`
		`done`
		`@@ -95,12 +99,7 @@`
		`for f in inchify_{InChI_TestSet,zzp} ; do`
		`sh ./${f}.sh`
		`done`
		`- %ifarch s390x`
		`- # https://bugzilla.redhat.com/show_bug.cgi?id=1930943`
		`- for t in its-.inc zzp-.inc ; do diff -u reference/$t $t \|\| : ; done`
		`- %else`
		`for t in its-.inc zzp-.inc ; do diff -u reference/$t $t ; done`
		`- %endif`
		`popd`

		`%files`
		`@@ -119,6 +118,9 @@`
		`%doc INCHI-1-DOC/*`

		`%changelog`
		`+ * Thu Nov 25 2021 Mamoru TASAKA <mtasaka@fedoraproject.org> - 1.0.6-3`
		`+ - Fix member read size mistake, especially on big endian (#1930943)`
		`+`
		`* Thu Jul 22 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.6-2`
		`- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild`